NeoNet app and dataset
Mapping radiocarbon dates from Late Mesolithic/Early Neolithic transition
Thomas Huet, Niccolo Mazzucco, Miriam Cubas, J. Francisco Gibaja, F. Xavier Oms, António Faustino Carvalho, Ana Catarina Basilio ¶
Figure 1: Preview of the published NeoNet C14 dates dataset, in red, covering the Late Mesolithic/Early Neolithic transition of the North Central-Western Mediterranean watershed
Presentation
The NeoNet app aims to contribute to the study the pioneering front of the farming live-style (i.e., Neolithic) by focusing our study on the mobile border between the Last Hunter-Gathers economy and the Early Neolithic (ca. 7,000 BC to 3,500 BC) in the Central-Western Mediterranean and European South Atlantic basins. The interactive web app facilitates the selection of absolute dates (radiocarbon dates) by providing selection tools for:
- spatial
- geographical region of interest (ROI)
- custom selection shape inside the ROI
- chronology
- date time span between a tpq and a taq in cal BC
- main periods (Middle Mesolithic, Late Mesolithic, Early Neolithic, …)
- date accuracy
- some type of material life duration (short like, long life or others)
- threshold of the maximum accepted standard deviation (SD)
The NeoNet app has been created in the frame of the NeoNet work group from a perspective of FAIR Science and collaborative working. It is still in development. This page is a tutorial for contributing and using the app. We will see how it works, what is the format dataset and what are our objectives
NeoNet app
The app is a RShiny hosted on the Università di Pisa server. The app is divided into five (5) panels:
- map panel: spatial filtering with selection menus on dates
- calib panel: calibration of the selected dates
- data panel: the whole dataset
- biblio panel: bibliographical references
- infos panel: credits and link to the webpage handbook of the app
To provide a handy user interface, NeoNet app joins a main dataset with to two correspondance tables:
- main dataset: 140_id00140_doc_elencoc14.tsv
- bibliographical references: id00140_doc_reference.bib
- material life duration: id00140_doc_thesaurus.tsv
So the NeoNet dataset is composed by two TSV files (dataframes with tab-separated values) and one BIB file (BibTex file, see: NeoNet dataset v.1
1. map panel
The panel map is a geographical window provided by the Leaflet package. This panel is used for selection of radiocarbon dates by location, by chronology, by quality of dates. Once selected, dates can be calibrated
Figure 2: The different menus of the map panel
The current functions are:
Fig. 2, red box, top-left radio button group C14 on map: allows to cluster dates by spatial proximities (Marker Clusters)
Fig. 2, pink box, top-right layer button: allows to change the basemap. By default, the basemap is OSM, an OpenStreetMap general basemap, but it can be switch to Topo, an ESRI topographical basemap
Fig. 2, green box, inline text: reactive count of selected dates and sites. The bottom table is a reactive DT package datatable listing all the dates within the map extent (ROI) and the optional selection menus (tpq/taq, material life duration, maximum SD, periods, selection shapes)
select by location
By default only the data within the window extent (ROI) will be selected. But selection shapes can be drawn inside this ROI to have a spatial intersection:
Fig. 2, black box, top-left draw toolbar: selection shapes, polygons and rectanges, can freeze the date selection inside a given ROI. They can be removed with the trash button. All the dates inside the ROI and selected with the others filters will be visible on the map, but only those inside the selections shapes will be calibrated
selection inside a shape, here a single polygon. Before shape selection: 190 sites and 895 dates. After shape selection: 13 sites and 68 dates
retrieve coordinates from the map
As said, the default basemap of the app is OSM. It offers a well documented basemap where archaeological sites are sometimes already located, like the Ligurian site of Grotta della Pollera. Clicking on the map show the lat/long coordinates of the current point (under the tpq/tap slider). These coordinates can then be copied and used to modify the NeoNet dataset
get coordinates by clicking on the map
select by chronology
select by dates quality
- Fig. 2, purple box, bottom-right checkboxes and slider: a group of menus for selection on the material life duration and max accepted SD:
- relatively to the duration of their material (short to long-life material)
- below a maximum accepted threshold for the standard deviations (SD) for the dates
calibrate one or various dates
The dates displayed in the table of the map panel will be calibrate when one of them has been clicked.
click on a date to calibrate a selected group of dates
2. calib panel
The panel calib is used for analysis. Calibration of selected dates are done on-the-fly with the R package rcarbon. If the dates are numerous (e.g., > 100) the computing time could take times, be patient.
calibration of selected radiocarbon dates
This date which have been clicked on the map panel will be shown bolded on the output figure
C14 group by filter
The c14 group by filter (Fig. 3, red box) allows to plot dates and to sum their probability densities depending on different levels of grouping:
by datation (by LabCode). Each radiocarbon date is plot separately (by default)
by site and layer (= SiteName and PhaseCode). Dates from the same site, having the same archaeological unit (layer, structure, etc.), are summed. See the PhaseCode field.
by site and period (= SiteName and Period). Dates from the same site, having the same period are summed
by period (= Period). Dates having the same period are summed
all C14. All dates are summed
Figure 3: The different menus of the calib panel
3. data panel
The complete dataset from the GitHub 140_140_id00140_doc_elencoc14.tsv file (ie, NeoNet dataset v.1). Today, the dataset counts 2506 dates:
| SiteName | Country | Period | PhaseCode | LabCode | C14Age | C14SD | Material | MaterialSpecies | tpq | taq | Longitude | Latitude | bib | bib_url |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cova dels Trocs | Spain | EN | Trocs I UE20 | Beta-284150 | 6070 | 40 | plant seed | Triticum sp. | -5205 | -4843 | 0.545612 | 42.45226 | Rojo et al. 2013 | Rojo13 |
| Grotta dei Piccioni | Italy | EN | Horizon early Phase of a middle Neolithic | Pl-46 | 6247 | 130 | wood charcoal | n/d | -5476 | -4853 | 13.962100 | 42.22190 | Ferrara et al. 1961 | https://doi.org/10.1017/S0033822200020889 |
| Les Breguieres | France | EN | Burial 8 | LTL-18523A | 5920 | 35 | human bone | Homo sapiens | -4898 | -4712 | 7.006350 | 43.59501 | Rivollat et al. 2020 | https://doi.org/10.1126/sciadv.aaz5344 |
| Cova del Frare | Spain | EN | c5 | Beta-325687 | 6020 | 40 | animal bone | Ovis aries | -5010 | -4796 | 2.019095 | 41.63733 | Navarrete et al., 2017 | https://doi.org/10.1002/oa.2598 |
| Molino Casarotto | Italy | MN | Site 4, Sqs 34-35-36/S-T-U, Cut 3B | R-762 | 5640 | 50 | wood charcoal | n/d | -4596 | -4354 | 11.539000 | 45.46560 | Alessio et al. 1974 | https://doi.org/10.1017/S0033822200059658 |
| Coro Trasito | Spain | EN | UE2013 | Beta-366546 | 6150 | 40 | animal bone | Bos taurus | -5215 | -4960 | 0.177973 | 42.59556 | Clemente Conte et al. 2014 | ClementeConte14 |
At first, these data were recorded in an Excel-like spreadsheet in order to facilitate their editing (filter, sorting, filling). As data came from various publications, a homogenization the different values (material, cultures, bibliographical references, etc.) has been done. The dataset mandatory fields are:
- SiteName: the site name
- coordinates (two fields)
- Longitude: in decimal degrees (ex:
1.0451) - Latitude: in decimal degrees (ex:
43.9213)
- Longitude: in decimal degrees (ex:
- Period: the main chronological period
- PhaseCode: a code for the dated stratigaphical unit and/or structure
- radiocarbon date (two fields)
- C14Age: uncalibrated date in BP
- C14SD: standard deviation (SD) of the radiocarbon date
- LabCode: the unique identifier of the radiocarbon date
- Material: a value from the material.life spreadsheet
- MaterialSpecies((#bd.materialspec): a specification of the field Material
- tpq: terminus post quem in calibrated BC
- taq: terminus ante quem in calibrated BC
- bibliographical references (two fields)
- bib: the short header
- bib_url: the DOI or the BibTex key
The recommended fields are:
- Culture: a specification of the field Period
mandatory fields
Here we explain more precisely some of the mandatory fields
SiteName
The most accepted version of the site name. For example: Cova de l'Or offers a better designation than L'Or or Or.
Longitude and Latitude
In decimal degrees and a minimal precision of four (4) decimal digits (ex: 1.0453, 43.9211). Since the NeoNet modeling is supra-regional, the app does not need to record dates with high accuracy geographical coordinates. At the minimum, this accuracy can be a location inside the departmental/county boundaries (how to retrieve better coordinates from the map)
Period
The period abbreviation. The main common periods considered here are: LM (Late Mesolithic), UM (Undefined Mesolithic), LMEN (Late Mesolithic/Early Neolithic), EN (Early Neolithic), MN (Middle Neolithic), LN (Late Neolithic), UN (Undefined Neolithic)
| periods | names | colors |
|---|---|---|
| EM | Early Mesolithic | #0000CF |
| MM | Middle Mesolithic | #1D1DFF |
| LM | Late Mesolithic | #3737FF |
| LMEN | Late Mesolithic/Early Neolithic | #6A6AFF |
| UM | Undefined Mesolithic | #8484FF |
| EN | Early Neolithic | #FF1B1B |
| EMN | Early/Middle Neolithic | #FF541B |
| MN | Middle Neolithic | #FF8D1B |
| LN | Late Neolithic | #FFC04D |
| UN | Undefined Neolithic | #E7E700 |
By default a different hexadecimal color is attributed to each period
PhaseCode
The PhaseCode field provides information about the archaeological context of a given date within a site. In most cases, it corresponds to an archaeological layer or structure. It is useful for layer/structure C14 grouping.
| PhaseCode |
|---|
| Zi -119 |
| unit 2 |
| Layer 3 inf |
| Storage pit A-3B19 |
| n/a |
| Layer IV |
At the site scale, these field values need to be homogeneized (for example: C.5 or layer 5 -> C5). The n/a value (i.e., not available) is reserved to dates without intra-site contextual information
LabCode
LabCode (i.e., laboratory code) should be unique. Their conventional syntax is ‘AbrevLab-number’, respecting the case letters (upper case and lower case). For example:
| LabCode |
|---|
| R-2705 |
| MC-2138 |
| MAMS-20437 |
| Beta-170714 |
| GrA-9789 |
| GrN-25046 |
See also the list of laboratories. Exceptionally, if a date has no LabCode – e.g., ‘Sep-H3 mix’ from Fontbregoua, 6082 +/- 35 BP – the convention is to use the PhaseCode (e.g., ‘Sep-H3 mix’) with an underscore as a prefix (e.g., ‘_Sep-H3 mix’) to get an unique key.
C14Age and C14SD
Conventional radiocarbon uncalibrated date (C14Age) and standard deviation error (C14SD). These two fields are used to calibrated the radiocarbon dates and calculate the tpq (terminus post quem) and taq (terminus ante quem).
| C14Age | C14SD |
|---|---|
| 6130 | 60 |
| 6570 | 40 |
| 6830 | 80 |
| 5320 | 35 |
| 6125 | 90 |
| 6175 | 40 |
Material
Material life duration are read from the GitHub 140_id00140_doc_thesaurus.tsv file (ie, NeoNet dataset v.1. The two fields show the material type (column 1) and the material life duration (column 2), for example:
| material.type | life.duration |
|---|---|
| food residue | |
| Mytilus | |
| FD | |
| Ovis aries | short.life |
| OR | short.life |
| Llavors | short.life |
Among these values, the published NeoNet dataset uses uniquely these ones:
| Material |
|---|
| animal bone |
| human and animal bone |
| human bone |
| n/a |
| n/d |
| organic |
| plant seed |
| shell |
| wood charcoal |
| wood charcoal or plant seeds |
The join between the main dataset and the material life thesaurus gives:
| material.type | life.duration |
|---|---|
| animal bone | short.life |
| human bone | short.life |
| n/a | |
| n/d | |
| organic | short.life |
| plant seed | short.life |
| shell | long.life |
| wood charcoal | long.life |
MaterialSpecies
bib and bib_url
Every radiocarbon date should be referenced with (i) a short plain text bibliographical reference (bib field) and (ii) a DOI or, when missing, a BibTex key (bib_url field). We favor the earliest mention of the radiocarbon date.
bib
The plain text that will be plot for each radiocarbon date under the bibliographical reference section. Basically the name of the author(s) and the publication year, for example Guilaine et al. 1993, Binder 2018 or Manen et Sabatier 2013. The values of this field can be the same for two different publications (e.g. Delibrias et al. 1982 refers to two different publications the same year)
bib_url
Either a DOI or a unique BibTeX key. We favor the DOI as a unique bibliographical reference. The values of this field should be unique for a single publication (e.g. the BibTeX keys Delibrias82 and Delibrias82a). For example:
| bib | bib_url |
|---|---|
| Bernabeu & Molina 2011 | Bernabeu11 |
| Mazzucco et al. 2020 | https://doi.org/10.1371/journal.pone.0232455.s002 |
| Manning et al. 2016 | https://doi.org/10.5334/joad.40 |
| Unpublished | Unpublished |
| Remicourt et al. 2014 | Remicourt14 |
| Utrilla et al. 2018 | https://doi.org/10.3989/tp.2018.12214 |
the DOI exists: Add the DOI value to the field. The DOI value starts with “
10”the DOI doesn’t exists: The complete bibliographical reference has to be included into the BIB document (eg., id00140_doc_reference.bib). In the BIB file, the bibliographical reference keyis the name of the first author and the two last digits of the year (eg.,
Guilaine93):
@book{Guilaine93,
title={Dourgne: derniers chasseurs-collecteurs et premiers {\'e}leveurs de la Haute-Vall{\'e}e de l'Aude},
author={Guilaine, Jean and Barbaza, Michel},
year={1993},
publisher={Centre d'anthropologie des soci{\'e}t{\'e}s rurales; Arch{\'e}ologie en Terre d'Aude}
}The same key of this reference is added to the bib_url field. For example, the key value Guilaine93 to map the main dataset to the BIB file.
| bib | bib_url |
|---|---|
| Guilaine et al. 1993 | Guilaine93 |
| … | … |
4. biblio panel
Bibliographical references are recorded in id00140_doc_reference.bib file. If only exist a BibTeX key, and no DOI, this file results of the join between the bib_url field of the C14 spreadsheet and the BIB file.
@Article{Binder18,
title = {Modelling the earliest north-western dispersal of Mediterranean Impressed Wares: new dates and Bayesian chronological model},
author = {Didier Binder and Philippe Lanos and Lucia Angeli and Louise Gomart and Jean Guilaine and Claire Manen and Roberto Maggi and Italo M Muntoni and Chiara Panelli and Giovanna Radi and others},
journal = {Documenta praehistorica},
volume = {44},
pages = {54-77},
year = {2018},
publisher = {University of Ljubljana Department of Archaeology},
}
@InProceedings{Briois09,
title = {L'abri de Buholoup: de l'{\'E}pipal{\'e}olithique au N{\'e}olithique ancien dans le piedmont central des Pyr{\'e}n{\'e}es},
author = {François Briois and Jean Vaquer},
booktitle = {De M{\'e}diterran{\'e}e et d'ailleurs...: m{\'e}langes offerts {\`a} Jean Guilaine},
pages = {141-150},
year = {2009},
}In the app, this BibTex file is rendered in HTML with an APA citation format (field long.ref) with the read.bib() and the markdown() functions (among others).
5. infos panel
Infos & credits
Adding and verifying data
Adding data
Follow the above recommendations
Verifying data
A large part of the work on the dataset is to check the quality and standardise the archaeological information. here are a workflow that can save you time:
retrieve the archaeological information of a given date
type the LabCode number of a date in Google Scholar, ex:
"OxA-14449"(with the quotes)
retrieve the bibtex or DOI of the date publication (cf. bib)
click on
Cite(red square) and then onBibTeX(green square) buttons
Then you can copy the bib reference as plain text and paste it in a file (any notepad, Word, Excel, etc.)
@article{moore2007project,
title={Project “Early farming in Dalmatia”: Danilo Bitinj 2004-2005 (Preliminary results)},
author={Moore, Andrew and Men{\dj}u{\v{s}}i{\'c}, Marko and Smith, Jennifer and Podrug, Emil},
journal={Vjesnik arheolo{\v{s}}kog muzeja u Zagrebu},
volume={40},
number={1},
pages={15--24},
year={2007},
publisher={Arheolo{\v{s}}ki muzej u Zagrebu}
}Developments
The NeoNet dataset will be extended to the European South Atlantic river basin (ie. Portugal, western Spain, and southwest France)